Is what you have electrically now totally stock other than the alternator?
If so, the only fusible link you need to worry about is the one that leads from the starter relay to the alternator batt + terminal. Everything else isn't going to draw any more power than it already was with the old alternator.
You can bypass it with a cable (4 gauge or so) directly from the battery positive terminal to the alternator batt + terminal. Fuse it as close to the battery as you can with a 150 amp fuse. You can unhook the old one or follow it through the loom and remove it if you want to.
Then, when you add accessories, just do it in a way that doesn't add any power draw through the old system.
Fuses and holders here are a lot cheaper than the ones at the fancy stereo store.
The poster above is right, a lot of times people don't fuse them, but as cheap as the fuses are, I don't see any reason not to.